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Related Experiment Videos

Web-accessible proteome databases for microbial research.

Klaus-Peter Pleissner1, Till Eifert, Sven Buettner

  • 1Max Planck Institute for Infection Biology, Berlin, Germany.

Proteomics
|June 10, 2004
PubMed
Summary
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A new proteome database integrates various data types, including two-dimensional electrophoresis (2-DE) and mass spectrometry (MS), to analyze microbial protein alterations. This system aids researchers in accessing and visualizing complex proteomic data.

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Analyzing proteomes is a major challenge in the post-genome era.
  • Classical proteomics uses two-dimensional electrophoresis (2-DE) and mass spectrometry (MS).
  • Novel techniques like isotope-coded affinity tag (ICAT)-liquid chromatography/mass spectrometry (LC/MS) offer new insights into protein alterations.

Purpose of the Study:

  • To develop a web-accessible database system for storing, integrating, and analyzing diverse proteomic data.
  • To provide a platform for microbial research, integrating experimental data with genomic and metabolic information.
  • To facilitate complex data analysis and visualization for researchers without extensive bioinformatics expertise.

Main Methods:

  • Construction of a proteome database integrating 2-DE/MS, ICAT-LC/MS, and functional classification data.

Related Experiment Videos

  • Inclusion of experimental data, mass spectra, and protein alteration data for specific microbial strains (e.g., BCG vs. H37Rv).
  • Utilizing the R language for on-the-fly data analysis and visualization, and a functional protein classification database (FUNC_CLASS).

    • Main Results:

    • The database integrates proteomic data from six microbial strains.
    • It enables complex queries for precise information on genes, proteins, and metabolic pathways for Mycobacterium tuberculosis and Helicobacter pylori.
    • The system supports high-level data analysis and visualization.

    Conclusions:

    • The developed proteome database system effectively manages and analyzes diverse microbial proteomic data.
    • It serves as a valuable resource for researchers and a template for a European Proteome Database of Pathogenic Bacteria.
    • The system democratizes access to complex proteomic data analysis and visualization.